Download Biosynthesis of the Antibiotic Nonribosomal Peptide Penicillin in

bioRxiv preprint first posted online Sep. 15, 2016; doi: http://dx.doi.org/10.1101/075325. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
Biosynthesis of the Antibiotic Nonribosomal Peptide Penicillin in Baker’s Yeast
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Ali R. Awan , Benjamin A. Blount , David J. Bell , Jack C. H. Ho , Robert M. McKiernan , Tom
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Ellis
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Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, UK
Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
SynbiCITE Innovation and Knowledge Centre, Imperial College London, London SW7 2AZ, UK
Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
Fungi are a valuable source of enzymatic diversity and therapeutic natural products
including antibiotics. By taking genes from a filamentous fungus and directing their
efficient expression and subcellular localisation, we here engineer the baker’s yeast
Saccharomyces cerevisiae to produce and secrete the antibiotic penicillin, a betalactam nonribosomal peptide. Using synthetic biology tools combined with long-read
DNA sequencing, we optimise productivity by 50-fold to produce bioactive yields that
allow spent S. cerevisiae growth media to have antibacterial action against
Streptococcus bacteria. This work demonstrates that S. cerevisiae can be engineered
to perform the complex biosynthesis of multicellular fungi, opening up the possibility
of using yeast to accelerate rational engineering of nonribosomal peptide antibiotics.
Many important therapeutics including key antibiotics are derived from compunds produced
by fungal organisms1, yet fungal enzymatic diversity is a largely untapped resource for cheap
biosynthesis of medical molecules and the potential for the discovery of novel therapeutics2, 3.
The baker’s yeast Saccharomyces cerevisiae is the most well-characterised unicellular fungi
and is also one of the main organisms used industrially for engineered biosynthesis4. Since
the advent of synthetic biology, S. cerevisiae has been genetically reprogrammed with diverse
enzymes from bacteria and eukaryotes to produce hundreds of different molecules of industrial
and therapeutic relevance including opiates and anti-malarial terpenoids5-9. A major class of
bioactive molecules found in fungi as well as in bacteria are the non-ribosomal peptides (Nrp).
These complex molecules, produced by large assembly-line enzymes called non-ribosomal
peptide synthetases (NRPS) include many front-line antibiotics including the classic betalactam antibiotic penicillin, naturally produced by filamentous fungi10, 11. However, despite a
wide range of known fungal NRPS genes and the plethora advanced genetic tools for S.
cerevisiae, there have been no reports of engineered beta-lactam antibiotic production from
this yeast.
Previously, Siewers et al. showed that co-expression of the Penicillium chrysogenum NRPS
gene pcbAB and an NPRS activator gene in S. cerevisiae led to cytosolic synthesis of amino-
bioRxiv preprint first posted online Sep. 15, 2016; doi: http://dx.doi.org/10.1101/075325. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
adipyl-cysteinyl-valine (ACV), the Nrp intermediate in the five gene P. chrysogenum pathway
of penicillin G (benzylpenicillin) biosynthesis12. While this revealed that the first step of betalactam production was possible in S. cerevisiae, the pathway to producing an active Nrp
antibiotic was incomplete. Using modular genetic tools to control enzyme expression, we
demonstrate here that correct subcellular localisation, along with expression optimisation of
the full five gene fungal pathway enables S. cerevisiae to synthesise benzylpenicillin. We
further demonstrate that bioactive benzylpenicillin is secreted by engineered yeast and that
spent culture media from the yeast has antibiotic activity against Streptococcus bacteria.
Results
Establishing biosynthesis and secretion of benzylpenicillin in S. cerevisiae
The benzylpenicillin pathway in P. chrysogenum consists of five genes converting cysteine,
valine and the non-canonical amino acid alpha-aminoadipic acid (AAA) into a beta-lactam
antibiotic via ACV (Fig 1a). The 11.3 kbp NRPS gene pcbAB and the NRPS activator gene
npgA required to produce ACV were first integrated into the S. cerevisiae BY4741 TRP1 locus
by inserting the two genes and the bidirectional GAL1/GAL10 promoters from the previously
described pESC-npgA-pcbAB plasmid12. ACV production in this strain (Sc.A1) was then
confirmed using Liquid Chromatography Mass Spectrometry (LCMS) comparing to a chemical
standard (Fig 1b). To complete the pathway and establish benzylpenicillin biosynthesis in S.
cerevisiae, we next required efficient expression of the remaining three P. chrysogenum
enzymes. However, as the final two steps of this pathway are known to naturally occur in the
peroxisome in P. chrysogenum13, we reasoned that cytoplasmic expression of all enzymes
would not suffice and that subcellular localisation would be the key to full synthesis. We
therefore took the step of tagging both pclA and penDE with the PTS1 tag14 to direct these
enzymes to co-localise in the peroxisome upon translation. To verify expression and
subcellular localisation of the enzymes, we constructed a single yeast plasmid expressing
pcbC, pclA and penDE each fused to a different fluorescent protein and verified expression
location by fluorescence microscopy (Fig 1c). To test whether simultaneous expression of all
five genes could yield benzylpenicillin production, we removed the fluorescent protein tags
from the three-gene plasmid, and transformed this into the Sc.A1 strain. The resulting strain
(Sc.P1) was shown to indeed produce low quantities of benzylpenicillin when measured by
LCMS (Fig 1d), and while the ACV Nrp intermediate was detected at equal amounts inside
and outside cells, benzylpenicillin was found predominantly in supernatant fractions,
suggesting active secretion of the antibiotic, as opposed to passive diffusion for ACV (Fig 1e).
bioRxiv preprint first posted online Sep. 15, 2016; doi: http://dx.doi.org/10.1101/075325. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
Figure 1. Production of benzylpenicillin by engineered S. cerevisiae. (a) Benzylpenicillin biosynthesis
requires a five enzyme pathway where alpha-aminoadipic acid (AAA), cysteine and valine are converted to
the tripeptide ACV by pcbAB and npgA. ACV is then converted to benzylpenicillin by pcbC, pclA and penDE.
(b) Strain Sc.A1 (S. cerevisiae BY4741 with genomically-integrated pcbAB and npgA genes) produces ACV
as observed by LCMS analysis. LCMS counts vs. retention time is shown for an ACV standard (light blue)
as well as for supernatant from an Sc.A1 culture (dark blue) and a BY4741 culture (black), both
supplemented with 5 mM AAA. (c) Subcellular localisation of enzymes encoded by pcbC, pclA and penDE
were verified by transforming S. cerevisiae BY4741 with a plasmid where each gene is tagged by fusion to
a different fluorescent protein. Fluorescence microscopy images show distribution for each fluorescent tag
(i-iii) and a composite (iv). Arrows indicate peroxisomes. pclA and penDE genes are tagged for peroxisomal
expression and pcbC is cytosolic. (d) To produce benzylpenicillin strain Sc.A1 was transformed with a
plasmid expressing pcbC, pclA and penDE to make strain Sc.P1. LCMS counts vs retention time is shown
for a benzylpenicillin standard (light green) as well as for supernatant from an Sc.P1 culture (dark green)
and an Sc.A1 culture (black), both supplemented with 5 mM AAA and 0.25 mM phenylacetic acid. (e)
Benzylpenicillin is secreted as shown by concentration-normalised log10 values of LCMS counts for cell
pellets and media for both ACV and benzylpenicillin from Sc.P1 cultures grown as in (d). Error bars show
standard deviation for three biological replicates.
Pathway optimisation with combinatorial library analysis by nanopore sequencing
Next, we sought to optimise production of benzylpenicillin in S. cerevisiae. One common
strategy for improving biosynthesis yields is to alter the expression levels of the pathway
enzymes, typically by changing the promoters for the corresponding genes15. This can
increase the flux through the pathway preventing the build-up of any inhibitory intermediates
but can also aid in finding efficient expression levels of enzymes that aid their correct folding
and subcellular localisation, both important considerations for this case. Therefore, using a
recently described modular cloning toolkit for yeast16 we constructed and tested hundreds of
different combinations of the benzylpenicillin pathway genes with different promoters known
to vary in strength and expression dynamics (Fig 2). We used this approach to first optimise
bioRxiv preprint first posted online Sep. 15, 2016; doi: http://dx.doi.org/10.1101/075325. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
the production of the ACV Nrp intermediate, and then the conversion of ACV to
benzylpenicillin. For the optimisation of ACV production, we cloned the two genes for ACV
biosynthesis with different pairs of promoters on a low-copy centromeric plasmid and
measured ACV yields from transformed BY4741 yeast by LCMS. All strains constructed
outperformed our Sc.A1 strain (~20 ng/mL) and one combination, pcbAB with pTDH3
promoter and npgA with pPGK1 promoter, generated a strain (Sc.A2) that even outperformed
yeast with the high-copy number pESC-npgA-pcbAB 2-micron plasmid containing strong
galactose-inducible promoters (~280 ng/mL vs ~70 ng/mL). We attribute these higher yields
to increased enzyme expression, presumably due to AT-rich sequences immediately
upstream of start codons on our plasmids. These sequences are known to improve translation
initiation efficiency in S. cerevisiae17.
Figure 2. Optimisation of benzylpenicillin production in S. cerevisiae. (a) Construction and sequencing
of a library with alternative promoters for pcbC, pclA and penDE. Ten different promoters of four categories
(strong, medium, weak or inducible) were randomly used to drive expression of each of the genes
responsible for conversion of ACV to benzylpenicillin. Plasmid libraries of single genes with different
promoters were initially constructed and then pooled to randomly assemble a multigene plasmid library.
Single gene and multigene libraries were subjected to MinION nanopore sequencing. The multigene library
was transformed into ACV producer Sc.A2 and transformants producing benzylpenicillin were Sanger
sequenced to reveal identity of promoters. (b) Concentrations of benzylpenicillin secreted into the
supernatant by the ten yeast strains selected from the promoter screen. The best producing strain makes
~5 ng/mL of benzylpenicillin as determined by LCMS. Under each bar, the category of the promoter in front
of each gene is shown. Error bars represent standard error of the mean from three biological replicates. (c)
Comparison of the percentage of promoters from each of the four categories for each pathway gene during
Golden Gate library construction (single and multiple gene steps) and among the ten benzylpenicillin
producing yeast strains as determined by DNA sequencing.
bioRxiv preprint first posted online Sep. 15, 2016; doi: http://dx.doi.org/10.1101/075325. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
To optimise conversion of ACV to benzylpenicillin, we next exploited one-pot combinatorial
DNA assembly using Golden Gate cloning to make a diverse library of high-copy plasmids in
which genes pcbC, pclA and penDE are each expressed from one of ten randomly assigned
promoters that span a range of strengths (Fig 2a). Eight different constitutive promoters and
two galactose-inducible promoters were included. The constitutive promoters were classified
as “strong” (4 total), “medium” (2 total) or “weak” (2 total) promoters according to their
characterisation in a previous study (Table S7)16. The resultant plasmid library with a
theoretical diversity of 1000 members was transformed into the Sc.A2 strain and a total of 160
colonies were individually screened by LCMS for benzylpenicillin production in YPD media
(Table S2).
From the screened colonies, the plasmids from ten strains showing detectable production of
benzylpenicillin were sequenced to determine the promoter combinations for pcbC, pclA and
penDE that direct efficient biosynthesis in S. cerevisiae. Sequencing revealed an apparent
over-representation of strong constitutive promoters at the pclA gene (10 out of 10) and of
medium constitutive promoters at the pcbC gene (5 out of 10) in strains with benzylpenicillin
production (Fig 2b). These results suggested that either a strong level of pclA expression is
always required for benzylpenicillin production in S. cerevisiae, or that our combinatorial DNA
assembly had an unintended bias for incorporation of these promoter parts into the final
plasmid library. To rule out any bias in our library assembly we used a MinION DNA sequencer
(Oxford Nanopore Technologies) to provide long-read sequencing of the assembly products
pooled from all stages in our plasmid library construction (Fig 2a). The ability of nanopore
sequencing to routinely return read lengths above 5 kb make it well suited to determining the
full-length products of modular DNA construction18. Two-directional (2D) reads of products
from multigene assembly revealed in vitro construction of over one hundred plasmids
containing different combinations of promoters in front the three pathway genes. No significant
bias for incorporation was seen during either of the DNA assembly steps compared to the
distribution expected by chance (Fig 2c), whereas a clear bias was seen for strong promoters
being required for pclA in all yeast strains able to perform benzylpenicillin biosynthesis (Fig
2c).
Antibiotic action of the spent yeast culture media
Optimisation of the biosynthesis pathway through combinatorial cloning with alternative
promoters led to a >50-fold increase in yields of secreted benzylpenicillin compared to our first
strain Sc.P1. The highest producer, strain Sc.P2, secretes benzylpenicillin into its growth
media at a concentration calculated to be around 5 ng/mL (Fig 2b). Using this strain, we next
sought to test whether benzylpenicillin secreted by engineered S. cerevisiae shows expected
bioRxiv preprint first posted online Sep. 15, 2016; doi: http://dx.doi.org/10.1101/075325. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
bioactivity. The secreted levels of benzylpenicillin are similar to those required for antibiotic
action against various bacteria such as Streptococcus pyogenes19. Therefore, to test the
bioactivity of the secreted benzylpenicillin, we diluted liquid cultures of S. pyogenes with spent
culture media from either Sc.P2 or from an inactivated version of Sc.P2 (Sc.P2x) that does
not produce benzylpenicillin (Fig 3a). Overnight growth of S. pyogenes was almost completely
inhibited in the presence of spent culture media from Sc.P2. By contrast, spent culture media
from the inactivated Sc.P2x strain resulted in normal growth of S. pyogenes (Fig 3b).
Simultaneous exposure of S. pyogenes to a range of concentrations of benzylpenicillin
standards revealed that the spent culture media from Sc.P2 had the antibiotic action
equivalent to 3 ng/mL of benzylpenicillin being present. This concentration was then verified
in parallel by LCMS analysis of the Sc.P2 culture media, demonstrating that the
benzylpenicillin secreted by S. cerevisiae has the same bioactivity as the commerciallyobtained standard.
Figure 3. Secreted benzylpenicillin is a bioactive antibiotic. (a) Schematic of the spent culture media
antibiotic activity test. (b) Fold change in OD600 of S. pyogenes cell cultures grown either in the presence
of increasing concentrations of benzylpenicillin standard over 18 hours (orange bars, left) or in the presence
of supernatant from benzylpenicillin producing yeast Sc.P2 (dark green bar, plus sign) and yeast Sc.P2x
with an inactive pcbAB gene (light green bar, minus sign). Concentration of benzylpenicillin in Sc.P2
supernatant as measured by LCMS is given above the dark green bar. Error bars show standard error of the
mean.
bioRxiv preprint first posted online Sep. 15, 2016; doi: http://dx.doi.org/10.1101/075325. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
Discussion
Our results demonstrate the first biosynthesis of a bioactive nonribosomal peptide (Nrp)
antibiotic from engineered S. cerevisiae yeast. After achieving production of benzylpenicillin,
we improved yields by optimising pathway enzyme expression and exploited long-read
nanopore sequencing to verify the combinatorial DNA assembly of our libraries to ascertain
the best combination of promoter strengths for increased yields. We observed that this always
required strong expression of the peroxisomally-located enzyme pclA. As engineered
heterologous biosynthesis of penicillin has only previously been observed with Hansenula
polymorpha, a methylotrophic yeast with large peroxisomes20, this suggests that boosting
peroxisomal expression further, for example by increasing peroxisome formation, by may be
a future approach to improve yields from S. cerevisiae. Further yield improvements could also
be achieved using other metabolic engineering strategies21, 22.
More generally, we view this achievement in S. cerevisiae as a paradigm for establishing
complex fungal biosynthesis pathways in a standard chassis organism used extensively in
research and industry. Give the impressive wealth of genetic tools and the ease of engineering
with this microbe, we see it as the ideal testbed for screening and diversifying fungal pathway
biosynthesis. We especially anticipate that expression and genetic manipulation of other
bioactive Nrp pathways in S. cerevisiae could advance the screening of engineered or newlydiscovered nonribosomal peptide synthetase (NRPS) enzymes from fungi. NRPS enzymes
represent a particularly attractive class of enzymes for engineering efforts as they are
inherently modular with each module region recognising one amino acid and incorporating it
into the Nrp product15, 23. NRPS modules incorporate both the standard 20 amino acids, as
well as hundreds of non-proteinogenic amino acids, including D-enantiomers24. Thus by
combining different modules together it should be possible make chimeric NRPS enzymes
that produce thousands of novel Nrp molecules predisposed by evolution for bioactivity25.
However, determining the structural boundaries of modules within natural NRPS enzymes has
so far proved extremely challenging due to the difficulty in obtaining structures for these
massive enzymes23, 26. An alternative approach to structure-guided mutagenesis is exhaustive
mutation and screening. Simple biological screens such as those based on the antibiotic
activity shown in this study could help pave the way towards true combinatorial biosynthesis
of novel bioactive Nrp molecules. Such endeavors are extremely important in light of
widespread resistance to antibiotics and the decreasing number of new antibiotics developed
through traditional means27.
bioRxiv preprint first posted online Sep. 15, 2016; doi: http://dx.doi.org/10.1101/075325. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
Acknowledgements
The authors are grateful to Dr Verena Siewers and Prof Jens Nielsen for their donation of the
pESC-npgA-pcbAB plasmid, and would like to thank Prof Shiranee Sriskandan and Kristin
Krohn Huse for their help handling S. pyogenes for the growth inhibition assay.
Funding
This work was funded in the UK by BBSRC awards BB/K006290/1 and BB/K019791/1 and
EPSRC award EP/L011573/1
Methods
Construction of strains
Strain Sc.A1 was made by replacing the TRP1 gene in BY4741 with the pcbAB-npgA segment
from the pESC-npgA-pcbAB plasmid from a previous study12. A URA3 gene from K. lactis was
integrated upstream of the pcbAB gene to allow genomic integration and the use of media
without uracil was used to enable comparison of the ACV production of this strain with that of
a BY4741 strain transformed with the ura-marked pESC-npgA-pcbAB plasmid. A full genetic
map of the altered TRP1 locus is provided as an annotated Genbank file in the Supplementary
Sequences. All other strains used in all experiments were constructed by transforming
plasmids into BY4741. A Zip file containing annotated Genbank files of all plasmids can be
requested.
Growth of Strains for ACV and penicillin production
For all ACV and penicillin producing experiments, cells were first grown overnight in synthetic
complete media minus the appropriate amino acids for selective pressure with glucose as the
carbon source. For plate based assays, cells were grown overnight at 700rpm at 30°C. For 50
mL falcon tube based assays, cells were grown at 225 rpm at 30°C. Overnight cultures were
then back-diluted into production media and grown at 20°C (216 rpm) for 20 hours (for plate
based assays) or until the OD600 reached between 0.6 and 0.8 (for 50 mL falcon tube assays).
Table S5 details the composition of production media for different experiments.
Fluorescence microscopy
Microscopy for Fig 1 was carried out with a Nikon Eclipse Ti, using the NIS Elements AR
software. The objective was set at 60x. Slides were fixed with yeast cells to visualise. The
excitation wavelengths for detection of Venus, mRuby2 and mTurquoise2 fluorescence were
535, 590 and 535 nM respectively.
Preparation of standards and samples for LCMS
For all LCMS experiments, standards were prepared as follows. ACV standards were
prepared by dissolving ACV (BACHEM H-4204) in water to a concentration of 10 ng/μL and
making three 10-fold dilutions. This gave four standards with concentrations of 10 ng/μL; 1
ng/μL; 100 pg/μL; 10 pg/μL. Benzylpenicillin standards were prepared by dissolving the
sodium salt of penicillin G (Sigma P3032) in water. The same concentrations were used for
benzylpenicillin as were used for ACV.
Cellular extracts for LCMS for the data in Fig 1 were prepared as follows. 30 mL of cell
culture was collected at an OD600 of 0.6. Cell culture was centrifuged at 7000 x g for 10
bioRxiv preprint first posted online Sep. 15, 2016; doi: http://dx.doi.org/10.1101/075325. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
minutes, and supernatant was either kept for LCMS (as in Fig 1d) or discarded. The cell pellet
was resuspended in 100 μL methanol. 50 μL of the resuspension was transferred to a
microcentrifuge tube with 25 μL of glass beads (Sigma G8772-100G) on ice. The tube was
then vortexed for 30 seconds and then placed on ice for 30 seconds, and these two steps
were repeated three times (for a total of four sets of vortexing and incubation on ice). The tube
was then centrifuged at 12,000 x g for 30 minutes, and 40 μL of supernatant was aliquoted to
a separate tube for LCMS measurement. Supernatants for LCMS from cultures grown in 96
well plates in Figure 2 were obtained by centrifuging plates at 3000 x g for 30 minutes.
LCMS
An LC/MS/MS method was developed for the measurement of penicillin-G and related
materials, using an Agilent 1290 LC and 6550 quadrupole time-of-flight (Q-ToF) mass
spectrometer with electrospray ionization (Santa Clara, CA). The LC column used was an
Agilent Zorbax Extend C-18, 2.1 x 50mm and 1.8um particle size. The LC buffers were 0.1%
formic acid in water and 0.1% formic acid in acetonitrile (v/v).
The gradient elution method is detailed in Table S6. Quantitation was based on the LC
retention times of standards and the area of accurately measured diagnostic fragment ion for
each molecule (Table S6). The protonated molecules of each analyte, [M+H]+, were targeted
and subjected to collision induced dissociation (collision energy 16eV), with product ions
accumulated throughout the analysis. Solutions of penicillin-G and ACV standards in water
were used to generate calibration curves.
The linear range of the method was determined by injecting standards over a range of
concentrations. The lower limit of detection (llod) was determined by the amount a sample
resulting in a peak with a signal-to-noise of 3:1. The lower limit of quantitation (lloq) was taken
to be the concentration of analyte that produced a signal-to-noise of 10:1. The llod and lloq for
penicillin-G were found to be on-column injections of 5 pg and 20 pg respectively.
Calculation of yield of ACV and benzylpenicillin from LCMS data
For both ACV and benzylpenicillin, pure chemical standards were run at the following
concentrations: 10 ng/mL, 100 ng/mL, 10 μg/mL, 100 μg/mL. The corresponding LCMS counts
for these standards were plotted against the concentrations of the standards and the linear
range of the resulting plot was used to construct a line of best fit in excel. The corresponding
line equation was used to obtain values for the yield in ng/mL of ACV and benzylpenicillin from
experimental samples based on the LCMS counts for these molecules.
Promoter screen for optimising conversion of ACV to penicillin
The assembly of multigene (pcbC, pclA, penDE) plasmids with ten randomised promoters was
split into two stages: assembly of single-gene constructs, then assembly of multigene
constructs. For single-gene construct assembly, an equimolar mix of all ten promoters was
made with a final concentration of 50 fM (referred to as “promoter mix”). This was used as a
type 2 plasmid according to the yeast toolkit specification16. Then, Golden Gate reactions were
set up with the following parts according to the Yeast Toolkit cassette plasmid Golden Gate
assembly protocol.
Each of the three reactions were transformed into E. coli, and for each of the three
transformation plates, transformant colonies were mixed together into a single overnight
culture each. From each of the three resulting cultures a plasmid library was prepared, of
which an aliquot was used to construct a pooled sample for nanopore sequencing (see section
bioRxiv preprint first posted online Sep. 15, 2016; doi: http://dx.doi.org/10.1101/075325. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
below). The three resulting single-gene plasmid libraries were used to set up a single
multigene golden gate reaction according to the yeast toolkit protocol.
This Golden Gate reaction was transformed into E. coli, and all transformant colonies
were mixed together into a single overnight culture. A multigene plasmid library was prepared
from this overnight culture. Part of this plasmid library was prepared for nanopore sequencing
(see section below), while 4 μg was used to transform into S. cerevisiae strain Sc.A2. The
resulting transformants were screened by LCMS for the production of benzylpenicillin and the
promoter regions of the multigene plasmids from producer strains were identified by Sanger
sequencing.
Nanopore sequencing library construction
To enrich for the penicillin pathway assembly DNA and remove assembly vector backbone
DNA, the multigene assembly library was digested with EcoRI and AlwNI. Restriction digest
products ranging from 5616 to 6117 bp were isolated by agarose gel electrophoresis and
purified using a QIAquick gel extraction kit (Qiagen). The single pathway gene assembly
libraries were similarly enriched by digestion with BsmBI and AlwnI. Restriction digest products
ranging from 2062 to 2229, 2549 to 2716 and 1885 to 20152 bp for the pcbC, pclA and penDE
assemblies, respectively, were purified.
Enriched assembly DNA for the multigene and single gene assemblies was quantified
on a Qubit 2.0 fluorometer (Thermo Fisher Scientific) using a Qubit dsDNA HS Assay Kit
(Thermo Fisher Scientific). The four samples were combined to a give an equimolar mix
(assuming a molecular weight for each assembly based on the mean promoter length) with a
total DNA content of 2.6 µg in 45 μL dH2O.
DNA underwent end repair using NEBNext FFPE DNA Repair Mix (M6630, New
England Biolabs) according to the manufacturer’s instructions. The repaired DNA was
recovered using Agincourt AMPure XP beads (A63880, Beckman Coulter), washed twice in
200 μL 70% ethanol and eluted in 46 μL dH2O. DNA was then dA-tailed using NEBNext Ultra
II End Repair/dA-Tailing Module (E7546, New England Biolabs) according to the
manufacturer’s instructions and recovered using Agincourt AMPure XP beads as before,
eluting in 30 μL dH2O.
The dA-tailed library DNA was then processed using Blunt/TA Ligase Master Mix
(M0367, New England Biolabs) and a Nanopore Sequencing Kit (SQK-NSK007, Oxford
Nanopore Technologies) according the manufacturer’s instructions to ligate adaptors and
tethers to the library. 50 μL Dynabeads MyOne Streptavidin C1 beads were washed twice in
buffer BBB (Nanopore Sequencing Kit) and then resuspended in 100 μL BBB. These beads
were then added to the processed DNA sample and mixed for 5 minutes at room temperature.
Beads were washed twice with 150 μL BBB before eluting the sample in 25 μL ELB (Nanopore
Sequencing Kit). The library was quantified by Qubit as before and yielded a total of 253 ng.
Nanopore sequencing
A fresh MinION R7 Flow Cell Mk I (FLO-MIN104, Oxford Nanopore Technologies) was loaded
into a MinION MK I (MIN-MAP002, Oxford Nanopore Technologies) and primed using a
Nanopore Sequencing Kit according to the manufacturer’s instructions. The sequencing mix
was generated by combining 75 μL RNB, 65 μL NFW and 4 μL Fuel Mix (Nanopore
sequencing kit) before adding 6 μL of the processed DNA library. This sequencing mix was
loaded into the flow cell and sequenced using the 48 hour sequencing script on MinKNOW
(Oxford Nanopore Technologies). After 18 hours, the script was stopped and a fresh
sequencing mix was prepared and loaded into the flow cell. The 48 hour sequencing script
bioRxiv preprint first posted online Sep. 15, 2016; doi: http://dx.doi.org/10.1101/075325. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
was then restarted. This reloading process was repeated after a further 4.5 hours. The
sequencing script was stopped once read acquisition had slowed to less than 1 successful
read in a 5 minute period.
Analysis of nanopore sequencing data
Oxford Nanopore's cloud-based Metrichor application '2D Basecalling for SQK-MAP006 v1.69'
was used to basecall data from a MinION run that used R7.3 chemistry. Poretools28
(https://github.com/arq5x/poretools) was used to extract sequence files and the program lastal
v658 (http://last.cbrc.jp/) was used to align the 2D reads to a database of all the potential
promoters and all combined CDS+terminators using options -s2 -T0 -Q0 -a1 -fTAB -e50*. To
remove reads corresponding to other DNA sequences present, the database was also
populated with sequences for AmpRTerm_AmpR_AmpRProm (part of the single assembly
plasmid backbone), His3Prom_His3Term_2Micron_KanRTerm_KanR_KanRProm (part of the
multiple assembly plasmid backbone), ColE1 (part of both the single and multiple assembly
plasmid backbone), and the lambda phage whole genome.
In order to build up a picture of which part of a plasmid each read represented, a custombuilt script ordered alignments first by read, then by read coordinates. It then identified reads
as originating from a particular plasmid by looking at plasmid regions in the database that each
read had aligned to. These identified reads were required to be a similar length (within 15%)
to the sum of lengths of regions of plasmids that they were aligned to. The script identified
digested multiple gene assemblies, digested single gene assemblies and, due to reduced
function of BsmBI, non-digested single assemblies. To be identified as a digested single gene
assembly, the read was also required to start and finish within 50 bp of the start and end of
the first and final regions respectively. This minimised the chance of misidentifying a multigene
assembly as a single gene assembly. The promoters at each position within these identified
reads were recorded.
*[-s2 use both query strands. -T0 local alignment. -Q0 use fasta as input. -a1 gap existence
cost of 1. -fTAB tabular output -e50 minimum alignment score of 50.]
S. pyogenes growth inhibition assay
An overnight culture of S. pyogenes (H584, M1 type) was grown for 24 hours at 37°C (5%
CO2) in Todd Hewitt Broth (THB). This culture was diluted in 10X THB to an optical density of
OD600 0.2. In separate wells of an optically-transparent 96 well plate (VWR 3596) 10 μL of
this solution was added to 90 μL of either a known concentration of benzylpenicillin dissolved
in 0.25 mM Phenylacetic acid or 90 μL of spent culture media from Sc.P2 or Sc.P2x strains
grown in production conditions. Sc.P2x is a variant of Sc.P2 known to not produce
benzylpenicillin due an inactive pcbAB caused by mutation in the coding region of the gene’s
terminal module region.
bioRxiv preprint first posted online Sep. 15, 2016; doi: http://dx.doi.org/10.1101/075325. The copyright holder for this preprint (which was
not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
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